def _time_from_ecat(self, ecat_file, ft_array):
shdrs = ecat.load(ecat_file).get_subheaders()
mlist = ecat.load(ecat_file).get_mlist()
framelist = mlist.get_series_framenumbers().values()
for fn, shdr in zip(framelist, shdrs.subheaders):
start = shdr['frame_start_time'] / 1000
duration = shdr['frame_duration'] / 1000
ft_array[fn, 1:4] = [start, duration, start + duration]
def _time_from_ecat(self, ecat_file, ft_array):
shdrs = ecat.load(ecat_file).get_subheaders()
mlist = ecat.load(ecat_file).get_mlist()
framelist = mlist.get_series_framenumbers().values()
for fn, shdr in zip(framelist, shdrs.subheaders):
start = shdr['frame_start_time'] / 1000
duration = shdr['frame_duration'] / 1000
ft_array[fn, 1:4] = [start, duration, start + duration]
def _time_from_ecat(self, ecat_file, ft_array):
""" fills in a fiels of empty ft_array using
data from the ecat mlist and subheaders"""
shdrs = ecat.load(ecat_file).get_subheaders()
mlist = ecat.load(ecat_file).get_mlist()
framelist = mlist.get_series_framenumbers().values()
for fn, shdr in zip(framelist, shdrs.subheaders):
start = shdr['frame_start_time'] / 1000
duration = shdr['frame_duration'] / 1000
idx = np.where(ft_array[:,0] == fn)
ft_array[idx, 1:] = [start, duration, start + duration]
def frametime_from_ecat(ecatf):
"""given an ecat file , finds timing info for each frame
Returns
-------
out : array
array holding framenumber, starttime, duration, endtime
in milliseconds
"""
img = ecat.load(ecatf)
shdrs = img.get_subheaders()
mlist = img.get_mlist()
framenumbers = mlist.get_series_framenumbers()
out = np.zeros((len(framenumbers), 4))
if shdrs.subheaders[0]['frame_start_time']== 16:
adj = 16
else:
adj = 0
for i, fn in framenumbers.items():
startt = shdrs.subheaders[i]['frame_start_time']
dur = shdrs.subheaders[i]['frame_duration']
out[i,0] = fn
out[i,1] = startt - adj
# fix adj, divide by 60000 to get minutes
out[i,2] = dur
out[i,3] = startt - adj + dur
out = out[out[:,0].argsort(),]
return out
def from_ecats(self, ecat_files, units=None):
"""Pulls timing info from ecat file(s) and stores in an array"""
if not hasattr(ecat_files, '__iter__'):
ecat_files = [ecat_files]
nframes = 0
for f in ecat_files:
x, y, z, nf = ecat.load(f).get_shape()
nframes += nf
empty_ft = self.generate_empty_protocol(nframes)
for ef in ecat_files:
self._time_from_ecat(ef, empty_ft)
self.data = np.array(empty_ft[0:,0:4]).astype(float)
# call to correct_data fails due to empty_ft dtype
if not units:
self.units = guess_units(self.data)
else:
self.units = units
try:
self.data = self.correct_data_order(self.data)
self._validate_frames()
except FrameError:
raise DataError('Bad data', self.data, ecat_files)
return self
def from_ecats(self, ecat_files, units=None):
"""Pulls timing info from ecat file(s) and stores in an array"""
if not hasattr(ecat_files, '__iter__'):
ecat_files = [ecat_files]
nframes = 0
for f in ecat_files:
x, y, z, nf = ecat.load(f).get_shape()
nframes += nf
empty_ft = self.generate_empty_protocol(nframes)
for ef in ecat_files:
self._time_from_ecat(ef, empty_ft)
self.data = np.array(empty_ft[0:, 0:4]).astype(float)
# call to correct_data fails due to empty_ft dtype
if not units:
self.units = guess_units(self.data)
else:
self.units = units
try:
self.data = self.correct_data_order(self.data)
self._validate_frames()
except FrameError:
raise DataError('Bad data', self.data, ecat_files)
return self
def _loadFile(self, path: str) -> None:
if path != self._FILE_CACHE:
e = ecat.load(path)
self._ECAT_CACHE = e.header
self._SUB_CACHE = e.get_subheaders().subheaders
self._FILE_CACHE = path
self.setManufacturer("Unknown", {})
self.resetMetaFields()
self.setupMetaFields(_ECAT.metafields)
self.testMetaFields()
